All Tutorials

  • Wed Oct 29, 1:30 pm - 4:00 pm
    402
    Walter Library

    The MathWorks, Inc. is presenting a free technical seminar demonstrating the use of MATLAB in bioinformatics research. Brian Madsen, M.S., Application Engineer Manager with The MathWorks, Inc. Will present the seminar. Check-in is from 1:00 to 1:30 and walk-ins are welcome. The seminar will include the following topics: covering sequence analysis and genotyping, access to proteomics data, analyzing microarray data, and pre-processing and analyzing MS data.


    Please register at www.mathworks.com/seminars/umn1029


  • Tue Oct 28, 1:30 pm - 3:30 pm
    575
    Walter Library

    The Crystallographic Object-Oriented Toolkit (Coot) is a free, academic software package mainly used by crystallographers to build, manipulate, refine and validate protein structures. Coot is similar to programs like O and Insight II in functionality, with the advantage of having many of the building and validation features automated. Coot also has the added benefit of being able to read the main binary files of CCP4 (.mtz files) directly to allow for easy map creation and refinement of the structure.


    This hands-on tutorial will bring the user up to speed on using Coot for the modeling portion of protein crystal structure refinement.


  • Mon Oct 27, 1:00 pm - 5:00 pm
    575
    Walter Library

    SIMULIA is the Dassault Systemes brand that delivers a scalable portfolio of Realistic Simulation solutions including Abaqus. The Abaqus Unified FEA product suite offers powerful and complete solutions for both routine and sophisticated engineering problems covering a vast spectrum of industrial applications. For example, in the automotive industry, engineering work groups are able to consider full vehicle loads, dynamic vibration, multibody systems, impact/crash, nonlinear static, thermal coupling, and acoustic-structural coupling using a common model data structure and integrated solver technology. Best-in-class companies are taking advantage of Abaqus Unified FEA to consolidate their processes and tools, reduce costs and inefficiencies, and gain a competitive advantage.


    The workshop will demonstrate how to do FEA of simple problems using Abaqus. The workshop will give students hands-on experience. The following topics may be covered: building models using Abaqus CAE; native geometry, geometry import, assemblies; finite element analysis using beam elements, shell elements, 3D solid elements; dynamic analysis using Abaqus Explicit; post-processing using Abaqus Viewer; incorporating contact in your model (if time allows).


  • Thu Oct 23, 1:00 pm - 4:00 pm
    575
    Walter Library

    Effectively using the large number of processors (1,000-100,000 and more) available on today?s (c. 2008) MPPs often requires careful structuring of the flow of information and computation for many computational tasks. Data output from thousands of processors can also present issues of efficiency and usable data format. We will discuss which MPI constructs kill scalability and techniques for producing scalable codes. Strategies and MPI constructs for overlapping interprocessor communication with computation will be discussed. We will also cover issues of weak and strong scaling, as well as efficient strategies for parallel IO.


  • Tue Oct 21, 1:00 pm - 3:00 pm
    402
    Walter Library

    MATLAB is a general computational platform for rapid development of programs. It also has several toolboxes that allow specialized computation on images. One such toolbox, the Image Processing Toolbox has hundreds of functions that can be used to perform operations on images.


    The various image processing operations can be classified into reading, processing, and writing images. We will begin the tutorial by performing simple image reading operations on jpeg, gif, etc. We will also discuss reading complex image formats like DICOM. We will then perform various image processing operations like filtering, visualization and analysis. We will then output these images to different formats to be read by other applications.


    We will conclude with a hands-on session using various example images. You are also welcome to bring specific questions and problems that you would like to discuss.


  • Thu Oct 16, 1:00 pm - 3:00 pm
    575
    Walter Library

    The Schrodinger software suite is a full-featured molecular modeling package designed to solve real world problems in pharmaceutical, biotechnology, and materials science research. One major advantage over other computational chemistry packages is that little to no text editing, scripting, or otherwise manual preparation of files is necessary to get started with the suite. This introduction to molecular modeling will focus on developing input and setting up calculations with the front-end GUI Maestro, various molecular mechanics and dynamics calculations, and the technical aspects of docking, quantum mechanics, and QM/MM studies.


  • Tue Oct 14, 1:00 pm - 3:00 pm
    402
    Walter Library

    Microarray is a powerful technology for biological exploration which enables users to simultaneously measure the level of activity of thousands of genes. It is becoming a routine experimental technique for life science research.


    This tutorial is an overview of this technology, which includes different microarray platforms, array design, data acquisition, data normalization, data analysis, and gene list interpretation. We will also introduce and compare several microarray software tools that MSI hosts.


  • Thu Oct 9, 1:00 pm - 3:00 pm
    575
    Walter Library

    Amira is a powerful visualization software package that enables data manipulation, geometry creation, and viewing in a meaningful format. This tutorial will describe the modular approach in Amira to build a visualization framework for different scientific data types. We will introduce concepts in computational geometry, modeling, and surfaces and volume rendering in Amira. This tutorial serves varying interest groups including medicine, biology, chemistry, physics, material sciences, geophysics, astronomy, and engineering.


  • Tue Oct 7, 1:00 pm - 3:00 pm
    402
    Walter Library

    The SAS system started out in the 1970s as a software package for statistical analysis, but is now a diverse family of integrated products that can be used as building blocks for constructing a complete data analysis system for data sets ranging from small to very large. In this tutorial, we provide an introduction to SAS.


    Among other skills, we will learn to load, create, and combine data sets in different ways, generate random samples, post results on the Web, and make simple plots. We will also cover writing basic code, using common statements and functions in SAS, and using statistical procedures. This tutorial is appropriate for people who have data that need to be processed and analyzed statistically.


  • Thu Oct 2, 1:00 pm - 4:00 pm
    575
    Walter Library

    Python is a general purpose programming language with a rich syntax and structure. It also has many modules specializing in various topics of interest to the scientific community like mathematical and textual processing. It is additionally used as an interface for numerous scientific packages such as NWChem and the Schrodinger suite. This tutorial is divided into two parts. The first will focus on an introduction to programming with Python. Topics covered will include control structures, data types, functions, mathematical and logical operators, and program input and output. The second part of the tutorial will cover advanced topics in Python like issuing commands to the Unix shell, reading and writing spreadsheet files, creating XML documents, and performing mathematical operations like a Pythonista.


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